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Genetic Variation in Phosphodiesterase (PDE) 7B in Chronic Lymphocytic Leukemia: Overview of Genetic Variants of Cyclic Nucleotide Pdes in Human Disease

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Genetic Variation in Phosphodiesterase (PDE) 7B in Chronic Lymphocytic Leukemia: Overview of Genetic Variants of Cyclic Nucleotide Pdes in Human Disease Journal of Human Genetics (2011) 56, 676–681 & 2011 The Japan Society of Human Genetics All rights reserved 1434-5161/11 $32.00 www.nature.com/jhg ORIGINAL ARTICLE Genetic variation in phosphodiesterase (PDE) 7B in chronic lymphocytic leukemia: overview of genetic variants of cyclic nucleotide PDEs in human disease Ana M Peiro´ 1,2, Chih-Min Tang1, Fiona Murray1,3, Lingzhi Zhang1, Loren M Brown1, Daisy Chou1, Laura Rassenti4, Thomas A Kipps3,4 and Paul A Insel1,3,4 Expression of cyclic adenosine monophosphate-specific phosphodiesterase 7B (PDE7B) mRNA is increased in patients with chronic lymphocytic leukemia (CLL), thus suggesting that variation may occur in the PDE7B gene in CLL. As genetic variation in other PDE family members has been shown to associate with numerous clinical disorders (reviewed in this manuscript), we sought to identify single-nucleotide polymorphisms (SNPs) in the PDE7B gene promoter and coding region of 93 control subjects and 154 CLL patients. We found that the PDE7B gene has a 5¢ non-coding region SNP À347C4T that occurs with similar frequency in CLL patients (1.9%) and controls (2.7%). Tested in vitro, À347C4T has less promoter activity than a wild-type construct. The low frequency of this 5¢ untranslated region variant indicates that it does not explain the higher PDE7B expression in patients with CLL but it has the potential to influence other settings that involve a role for PDE7B. Journal of Human Genetics (2011) 56, 676–681; doi:10.1038/jhg.2011.80; published online 28 July 2011 Keywords: cAMP; chronic lymphocytic leukemia; cyclic nucleotide phosphodiesterases; PDE7B single-nucleotide polymorphisms INTRODUCTION 410-fold in peripheral blood mononuclear cells of patients with Cyclic nucleotide phosphodiesterases (PDEs), a superfamily of CLL.16 We thus set out to determine if the increased expression of enzymes divided into 11 families (PDE1–11), several with multiple PDE7B in CLL patients might result from genetic variation in the isoforms,1,2 hydrolyze cyclic adenosine monophosphate (cAMP) and coding sequence or 5¢ untranslated region (5¢ UTR) of the PDE7B cyclic guanosine monophosphate (cGMP), and thereby have a crucial gene. We began these studies with the knowledge that genetic varia- role in termination of cyclic nucleotide-mediated signaling, in parti- tion, in particular single-nucleotide polymorphisms (SNPs), had been cular signaling by drugs that regulate the generation of cAMP and identified in certain PDE family members, and suggested to contribute cGMP.3 In addition, PDEs, including specific PDE isoforms, have been to clinical disorders, such as schizophrenia (for example, PDE4B),17–19 used as drug targets. Several PDEs, including PDE4, PDE7 and PDE8, stroke (for example, PDE4D)20 and retinitis pigmentosa (for example, preferentially hydrolyze cAMP.4 In spite of their importance in the PDE6A and PDE6B),21 but evidence regarding such genetic variation regulation of cyclic nucleotides, the mechanisms that regulate the for other PDEs is limited. We thus set out to identify genetic variants expression of PDE genes are not well defined. For example, regions in in the PDE7B gene and to test the hypothesis that genetic variation the promoter that regulate activity have only been identified for a might contribute to the increased PDE7B mRNA expression in CLL limited number of PDE genes5 and details regarding events involved in and to the pathophysiology of CLL with implications for the possible PDE gene expression are not well understood. Increases in cAMP can use of inhibitors of PDE7B in the treatment of CLL. By sequencing the regulate the expression of certain PDEs, in particular via action of the 5¢ UTR of the PDE7B gene, we identified a variant that decreases cAMP-response element-binding protein or the inducible cAMP early promoter activity. In addition, in this article, we place our findings for repressor,6–9 and in addition, glucocorticoids can transcriptionally PDE7B in the context of genetic variation of other human PDEs. inhibit PDE expression.10,11 Our interest in PDE gene expression arose from studies of patients MATERIALS AND METHODS with chronic lymphocytic leukemia (CLL), the most common Patient selection and sample preparation 12 leukemia in North American and European adults. We found that We evaluated samples from 154 CLL patients followed by the CLL Research mRNA and protein expression of PDE7B, a cAMP-specific PDE Consortium and 93 healthy donors at the University of California, San Diego. predominantly expressed in brain and lymphocytes,13–15 are increased Following informed consent, blood was collected from the healthy donors and 1Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA; 2Department of Clinical Pharmacology, Hospital General Universitario de Alicante, Alicante, Spain; 3Department of Medicine, University of California, San Diego, La Jolla, CA, USA and 4Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Correspondence: Dr PA Insel, Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA 92093-0636,USA. E-mail: [email protected] Received 29 April 2011; revised 16 June 2011; accepted 17 June 2011; published online 28 July 2011 Single-nucleotide polymorphism in the PDE7B promoter AM Peiro´ et al 677 Table 1 Demographic data of CLL patients and control subjects who have WT PDE7B or those with the À347C4TSNP Control CLL SNP (n¼4) WT (n¼89) Total (n¼93) SNP (n¼6) WT (n¼148) Total (n¼154) Male:female 4:0 73:16 77:16 4:2 92:56 96:58 Age (years) 42±855±13 55±13 64±12 62±10 62±10 IgVH (%) — — — 95±495±996±4 ZAP-70 level (%) — — — 12±18 24±28 23±27 WBC (cells mlÀ1 Â1000) — — — 105±50 87±121 88±119 Abbreviations: CLL, chronic lymphocytic leukemia; IgVH, immunoglobulin heavy chain variable; PDE7B, phosphodiesterase 7B; SNP, single-nucleotide polymorphism; WBC, white blood cell; WT, wild type; ZAP-70, 70-kDa zeta-associated protein. Data for age, IgVH%, Zap70 and WBC are shown as mean±s.d. from patients who satisfied diagnostic and immunophenotypic criteria for CLL. Table 2 Gender-allele frequency analysis of expression of the The University of California, San Diego, Institutional review board approved À347C4T variant of PDE7B these studies and the CLL Research Consortium approved the procurement of the samples, with all approvals in accordance with the Declaration of Helsinki. Gender Number Alleles SNP/total alleles Diagnosis of CLL was based on morphological and immunophenotyping criteria.22 Patients with CLL were also categorized by the expression of 70-kDa Male zeta-associated protein.23–25 Mononuclear cells were isolated using a Ficoll CLL 96 4 4/192 (2%) gradient and then frozen in fetal calf serum plus 10% dimethyl sulfoxide before Control 77 5 5/154 (3.3%) storage in liquid N2. The 70-kDa zeta-associated protein expression was deter- Total 173 9 9/346 (2.6%)* mined by flow cytometry of mononuclear cells. PCR was used to assess the immunoglobulin heavy chain variable gene family. Table 1 shows demographic Female data, heavy chain variable and the 70-kDa zeta-associated protein status. CLL 58 2 2/116 (1.7%) Control 16 0 0/32 (0%) Genomic DNA and RNA extraction, PCR and sequencing Total 74 2 2/148 (1.4%)* Genomic DNA and RNA were prepared using isolation kits for blood cells Abbreviations: CLL, chronic lymphocytic leukemia; PDE7B, phosphodiesterase 7B; SNP, single- (Qiagen, Valencia, CA, USA). The complementary DNA (cDNA) was generated nucleotide polymorphism. using the Superscript III cDNA synthesis system (Invitrogen, Carlsbad, CA, *P-values were 40.1 for differences in expression of the variant between control males and males with CLL and between males and females. USA) according to the manufacturer’s instructions. We sought to identify genetic variants within the putative PDE7B (NC_000006.11) promoter and coding regions as follows: (a) PDE7B gene promoter, the region 700 bp * upstream and 300 bp downstream of the transcription start site of PDE7B 8 ** was amplified; this resulted in a 1-kb PCR product (P1; forward primer: 5¢-CACCATAGCCTTGCTTCTTGA-3¢; reverse primer, 5¢-TGGCAGTTCTGTG 7 ACCTTTG-3¢). (b) PDE7B coding region (304 to 1656 nt), the full-length 6 ** cDNA of PDE7B was amplified in two PCR products, P2 from 276 to 1165 bp 5 (forward primer: 5¢-CTGGAGAAGTTGCTGGATTCT-3¢; reverse primer: 5¢-ATT 4 CATTCTGCCTGTTGATGTCT-3¢) and P3 from 1074 to 1870 bp (forward primer: 5¢-CTCTGGACATCATGCTTGGA-3¢; reverse primer: 5¢-CTCCCACG 3 TTACTGAATGGAG-3¢). PCR amplifications were performed (AccuPower PCR 2 Premix; Bioneer, Alameda, CA, USA) using standard procedures with 50 ng of Activity Luciferase 1 genomic DNA product (P1) or 200 ng of cDNA (P2–3), in a total volume of vector) increase over (fold 20 mLcontaining10mM Tris-HCl (pH 9.0), 40 mM KCl, 1.5 mM MgCl ,1U 0 2 vec WT SNP DNA polymerase, 1.5 mM deoxyribonucleotide triphosphate and 0.5 mM each specific primer. PCR cycling conditions were: initial denaturing at 95 1Cfor Figure 1 Impact of the À347C and À347T genotypes on PDE7B promoter 5 min (P1) or 2 min (P2–3) followed by 35 cycles of denaturing at 94 1Cfor function. pGL4 luciferase reporter constructs containing a 1-kb phospho- 40 s; annealing at 59 1C(P1),551C(P2)or571C (P3) for 40 s; extension at diesterase 7B promoter with the À347C (WT) or À347T (SNP) genotype 72 1C for 57 s (P1), 59 s (P2) or 58 s (P3); and a final extension step at 72 1Cfor were transfected into HEK293 cells. Vec, the promoter-less pGL4, was used 5 min. DNA Clean & Concentrator TM-5 kit (D4003 lt 0940 BW) and Centri- as a control and its luciferase activity was defined as 1. The data represent sep columns (Zymo Research, Orange, CA, USA) were used to purify PCR the mean±s.d.
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